On Wed, 8 Nov 2017, Susan Fairley wrote:
Thanks for letting me know about this.
I’ve had a (very) quick look and the samtools view -H command is working for me
with v1.2.
[alignment]:samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 1.2 (using htslib 1.2.1)
[alignment]:samtools view -H
SC_GMFUL5306366.alt_bwamem_GRCh38DH.20151208.FULA.gambian_lowcov.cram
@HD VN:1.5 SO:coordinate
Any thoughts on what is causing this and the best way to address it are
welcome.
Is that the file on the FTP site, or a different copy? If it's a
different copy, you need to upload it to the FTP site to replace the
broken file. It would also be a good idea to check the rest for the
similar problems.
Rob Davies r...@sanger.ac.uk
The Sanger Institute http://www.sanger.ac.uk/
Hinxton, Cambs., Tel. +44 (1223) 834244
CB10 1SA, U.K. Fax. +44 (1223) 494919
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